Ricchiuto Piero, Iwata Hiroshi, Yabusaki Katsumi, Yamada Iwao, Pieper Brett, Sharma Amitabh, Aikawa Masanori, Singh Sasha A
Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
J Proteomics. 2015 Oct 14;128:132-40. doi: 10.1016/j.jprot.2015.07.024. Epub 2015 Jul 29.
Isobaric mass tagging (IMT) methods enable the analysis of thousands of proteins simultaneously. We used tandem mass tagging reagents (TMT™) to monitor the relative changes in the proteome of the mouse macrophage cell line RAW264.7 at the same six time points after no stimulation (baseline phenotype), stimulation with interferon gamma (pro-inflammatory phenotype) or stimulation with interleukin-4 (anti-inflammatory phenotype). The combined TMT datasets yielded nearly 12,000 protein profiles for comparison. To facilitate this large analysis, we developed a novel method that combines or multiplexes the separate IMT (mIMT) datasets into a single super dataset for subsequent model-based clustering and co-regulation analysis. Specially designed visual High Throughput Screening (visHTS) software screened co-regulated proteins. visHTS generates an interactive and visually intuitive color-coded bullseye plot that enables users to browse the cluster outputs and identify co-regulated proteins.
等压质量标记（IMT）方法能够同时分析数千种蛋白质。我们使用串联质量标记试剂（TMT™）来监测小鼠巨噬细胞系RAW264.7在无刺激（基线表型）、用γ干扰素刺激（促炎表型）或用白细胞介素-4刺激（抗炎表型）后的相同六个时间点的蛋白质组相对变化。合并后的TMT数据集产生了近12000个蛋白质谱用于比较。为便于进行这种大规模分析，我们开发了一种新方法，将单独的IMT（mIMT）数据集合并或复用成一个单一的超级数据集，用于后续基于模型的聚类和共调控分析。经过特殊设计的可视化高通量筛选（visHTS）软件筛选共调控蛋白质。visHTS生成一个交互式且视觉直观的彩色编码靶心图，使用户能够浏览聚类输出并识别共调控蛋白质。
